
%%capture
!pip install cadcad


import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from cadCAD.configuration import Experiment
from cadCAD.configuration.utils import config_sim
from cadCAD.engine import ExecutionMode, ExecutionContext, Executor


initial_conditions = {
    'prey_population': 100,
    'predator_population': 15
    }

params = {
    "prey_birth_rate": [1.0],
    "predator_birth_rate": [0.01],
    "predator_death_const": [1.0],
    "prey_death_const": [0.03],
    "dt": [0.1] # Precision of the simulation. Lower is more accurate / slower
}

simulation_parameters = {
    'N': 7,
    'T': range(200),
    'M': params
}


def p_predator_births(params, step, sL, s):
  dt = params['dt']
  predator_population = s['predator_population']
  prey_population = s['prey_population']
  birth_fraction = params['predator_birth_rate'] + np.random.random() * 0.0002
  births =  birth_fraction * prey_population * predator_population * dt
  return {'add_to_predator_population': births}


def p_prey_births(params, step, sL, s):
  dt = params['dt']
  population = s['prey_population']
  birth_fraction = params['prey_birth_rate'] + np.random.random() * 0.1
  births =  birth_fraction * population * dt
  return {'add_to_prey_population': births}


def p_predator_deaths(params, step, sL, s):
  dt = params['dt']
  population = s['predator_population']
  death_rate = params['predator_death_const'] + np.random.random() * 0.005
  deaths = death_rate * population * dt
  return {'add_to_predator_population': -1.0 * deaths}


def p_prey_deaths(params, step, sL, s):
  dt = params['dt']
  death_rate = params['prey_death_const'] + np.random.random() * 0.1
  prey_population = s['prey_population']
  predator_population = s['predator_population']
  deaths = death_rate * prey_population * predator_population * dt
  return {'add_to_prey_population': -1.0 * deaths}


def s_prey_population(params, step, sL, s, _input):
    y = 'prey_population'
    x = s['prey_population'] + _input['add_to_prey_population']
    return (y, x)


def s_predator_population(params, step, sL, s, _input):
    y = 'predator_population'
    x = s['predator_population'] + _input['add_to_predator_population']
    return (y, x)


partial_state_update_blocks = [
    { 
        'label': 'Predator dynamics',
        'ignore': False,
        'debug': True,
        'policies': {
            'predator_births': p_predator_births,
            'predator_deaths': p_predator_deaths
        },
        'variables': {
            'predator_population': s_predator_population            
        }
    },
    {
        'label': 'Prey dynamics',
        'ignore': False,
        'policies': {
            'prey_births': p_prey_births,
            'prey_deaths': p_prey_deaths
        },
        'variables': {
            'prey_population': s_prey_population
        }
    }
]


sim_config = config_sim(simulation_parameters)

exp = Experiment()
exp.append_configs(sim_configs=sim_config, 
                   initial_state=initial_conditions,
                   partial_state_update_blocks=partial_state_update_blocks)


from cadCAD import configs
exec_mode = ExecutionMode()
exec_context = ExecutionContext(exec_mode.local_mode)
executor = Executor(exec_context=exec_context, configs=configs) 
(records, tensor_field, _) = executor.execute()

                  ___________    ____
  ________ __ ___/ / ____/   |  / __ \
 / ___/ __` / __  / /   / /| | / / / /
/ /__/ /_/ / /_/ / /___/ ___ |/ /_/ /
\___/\__,_/\__,_/\____/_/  |_/_____/
by cadCAD

Execution Mode: local_proc
Configuration Count: 1
Dimensions of the first simulation: (Timesteps, Params, Runs, Vars) = (200, 5, 7, 2)
Execution Method: local_simulations
SimIDs   : [0, 0, 0, 0, 0, 0, 0]
SubsetIDs: [0, 0, 0, 0, 0, 0, 0]
Ns       : [0, 1, 2, 3, 4, 5, 6]
ExpIDs   : [0, 0, 0, 0, 0, 0, 0]
Execution Mode: parallelized
Total execution time: 0.18s


import plotly.express as px


df = pd.DataFrame(records)

fig = px.line(df,
              x=df.prey_population,
              y=df.predator_population,
              color=df.run.astype(str))

fig.show()


%%capture
!pip install cadCAD_diagram==0.0.1.2


from cadCAD_diagram import diagram_from_config
from cadCAD import configs
diagram_from_config(configs[0])

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
~/.local/lib/python3.9/site-packages/graphviz/backend.py in run(cmd, input, capture_output, check, encoding, quiet, **kwargs)
    163     try:
--> 164         proc = subprocess.Popen(cmd, startupinfo=get_startupinfo(), **kwargs)
    165     except OSError as e:

/usr/local/lib/python3.9/subprocess.py in __init__(self, args, bufsize, executable, stdin, stdout, stderr, preexec_fn, close_fds, shell, cwd, env, universal_newlines, startupinfo, creationflags, restore_signals, start_new_session, pass_fds, user, group, extra_groups, encoding, errors, text, umask)
    950 
--> 951             self._execute_child(args, executable, preexec_fn, close_fds,
    952                                 pass_fds, cwd, env,

/usr/local/lib/python3.9/subprocess.py in _execute_child(self, args, executable, preexec_fn, close_fds, pass_fds, cwd, env, startupinfo, creationflags, shell, p2cread, p2cwrite, c2pread, c2pwrite, errread, errwrite, restore_signals, gid, gids, uid, umask, start_new_session)
   1822                         err_msg = os.strerror(errno_num)
-> 1823                     raise child_exception_type(errno_num, err_msg, err_filename)
   1824                 raise child_exception_type(err_msg)

FileNotFoundError: [Errno 2] No such file or directory: 'dot'

During handling of the above exception, another exception occurred:

ExecutableNotFound                        Traceback (most recent call last)
~/.local/lib/python3.9/site-packages/IPython/core/formatters.py in __call__(self, obj)
    343             method = get_real_method(obj, self.print_method)
    344             if method is not None:
--> 345                 return method()
    346             return None
    347         else:

~/.local/lib/python3.9/site-packages/graphviz/files.py in _repr_svg_(self)
    142 
    143     def _repr_svg_(self):
--> 144         return self.pipe(format='svg').decode(self._encoding)
    145 
    146     def pipe(self, format=None, renderer=None, formatter=None, quiet=False):

~/.local/lib/python3.9/site-packages/graphviz/files.py in pipe(self, format, renderer, formatter, quiet)
    167         data = text_type(self.source).encode(self._encoding)
    168 
--> 169         out = backend.pipe(self._engine, format, data,
    170                            renderer=renderer, formatter=formatter,
    171                            quiet=quiet)

~/.local/lib/python3.9/site-packages/graphviz/backend.py in pipe(engine, format, data, renderer, formatter, quiet)
    246     """
    247     cmd, _ = command(engine, format, None, renderer, formatter)
--> 248     out, _ = run(cmd, input=data, capture_output=True, check=True, quiet=quiet)
    249     return out
    250 

~/.local/lib/python3.9/site-packages/graphviz/backend.py in run(cmd, input, capture_output, check, encoding, quiet, **kwargs)
    165     except OSError as e:
    166         if e.errno == errno.ENOENT:
--> 167             raise ExecutableNotFound(cmd)
    168         else:
    169             raise

ExecutableNotFound: failed to execute ['dot', '-Kdot', '-Tsvg'], make sure the Graphviz executables are on your systems' PATH

<graphviz.dot.Digraph at 0x7fd319196850>

Diagrams for cadCAD model structure through cadCAD_diagram¶

Dependences¶

Definitions¶

Initial conditions and parameters¶

Policies¶

State update functions¶

State update blocks¶

Configuration and Execution¶

Results¶

Diagram¶